Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement.

A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.

Using UHF proximity loggers to quantify male–female interactions: A scoping study of estrous activity in cattle

Reproductive efficiency is an important determinant of profitable cattle breeding systems and the success of assisted reproductive techniques (ART) in wildlife conservation programs. Methods of estrous detection used in intensive beef and dairy cattle systems lack accuracy and remain the single biggest issue for improvement of reproductive rates and such methods are not practical for either large-scale extensive beef cattle enterprises or free-living mammalian species. Recent developments in UHF (ultra high frequency) proximity logger telemetry devices have been used to provide a continuous pair-wise measure of associations between individual animals for both livestock and wildlife. The objective of this study was to explore the potential of using UHF telemetry to identify the reproductive cycle phenotype in terms of intensity and duration of estrus. The study was conducted using Belmont Red (interbred Africander Brahman Hereford–Shorthorn) cattle grazing irrigated pasture on Belmont Research Station, northeastern Australia. The cow-bull associations from three groups of cows each with one bull were recorded over a 7-week breeding season and the stage of estrus was identified using ultrasonography. Telemetry data from bull and cows, collected over 4 8-day logger deployments, were log transformed and analyzed by ANOVA. Both the number and duration of bull-cow affiliations were significantly (P < 0.001) greater in estrous cows compared to anestrus cows. These results support the development of the UHF technology as a hands-off and noninvasive means of gathering socio-sexual information on both wildlife and livestock for reproductive management.

Applications of pedigree-based genome mapping in wheat and barley breeding programs.

The aim of the pedigree-based genome mapping project is to investigate and develop systems for implementing marker assisted selection to improve the efficiency of selection and increase the rate of genetic gain in breeding programs. Pedigree-based whole genome marker application provides a vehicle for incorporating marker technologies into applied breeding programs by bridging the gap between marker-trait association and marker implementation. We report on the development of protocols for implementation of pedigree-based whole genome marker analysis in breeding programs within the Australian northern winter cereals region. Examples of applications from the Queensland DPI&F wheat and barley breeding programs are provided, commenting on the use of microsatellites and other types of molecular markers for routine genomic analysis, the integration of genotypic, phenotypic and pedigree information for targeted wheat and barley lines, the genomic impacts of strong selection pressure in case study pedigrees, and directions for future pedigree-based marker development and analysis.

Integrating grazing and forage systems on marginal cropping lands

Planned grazing systems are being introduced to beef cattle enterprises across the marginal cropping lands of Queensland, as they are on more extensive grazing properties. Systems range from continuous grazing with opportunistic summer rest periods to cell systems with more than 60 paddocks. The aim of planned grazing is to increase production, improve sustainability and increase economic viability from both the pastured and cropping lands of a property. Managing the more intensive grazing systems on native or sown pastures with strategic summer and winter forage crops is a challenge under the variable rainfall conditions. Under favourable conditions, integrating summer and winter crops with summer-growing grass-based pastures offers a wider range of options for breeding, finishing and marketing cattle. The integration of pasture grazing systems with opportunistic forage cropping systems on marginal cropping lands is discussed, and a current research project assessing grazing systems is described.

Simulating pasture growth rates in Australian and New Zealand grazing systems

DairyMod, EcoMod, and the SGS Pasture Model are mechanistic biophysical models developed to explore scenarios in grazing systems. The aim of this manuscript was to test the ability of the models to simulate net herbage accumulation rates of ryegrass-based pastures across a range of environments and pasture management systems in Australia and New Zealand. Measured monthly net herbage accumulation rate and accumulated yield data were collated from ten grazing system experiments at eight sites ranging from cool temperate to subtropical environments. The local climate, soil, pasture species, and management (N fertiliser, irrigation, and grazing or cutting pattern) were described in the model for each site, and net herbage accumulation rates modelled. The model adequately simulated the monthly net herbage accumulation rates across the range of environments, based on the summary statistics and observed patterns of seasonal growth, particularly when the variability in measured herbage accumulation rates was taken into account. Agreement between modelled and observed growth rates was more accurate and precise in temperate than in subtropical environments, and in winter and summer than in autumn and spring. Similarly, agreement between predicted and observed accumulated yields was more accurate than monthly net herbage accumulation. Different temperature parameters were used to describe the growth of perennial ryegrass cultivars and annual ryegrass; these differences were in line with observed growth patterns and breeding objectives. Results are discussed in the context of the difficulties in measuring pasture growth rates and model limitations.

A systems evaluation of high-input management using fortified molasses for beef production in Australia's dry tropics

The potential of beef producers to profitably produce 500-kg steers at 2.5 years of age in northern Australia's dry tropics to meet specifications of high-value markets, using a high-input management (HIM) system was examined. HIM included targeted high levels of fortified molasses supplementation, short seasonal mating and the use of growth promotants. Using herds of 300-400 females plus steer progeny at three sites, HIM was compared at a business level to prevailing best-practice, strategic low-input management (SLIM) in which there is a relatively low usage of energy concentrates to supplement pasture intake. The data presented for each breeding-age cohort within management system at each site includes: annual pregnancy rates (range: 14-99%), time of conception, mortalities (range: 0-10%), progeny losses between confirmed pregnancy and weaning (range: 0-29%), and weaning rates (range: 14-92%) over the 2-year observation. Annual changes in weight and relative net worth were calculated for all breeding and non-breeding cohorts. Reasons for outcomes are discussed. Compared with SLIM herds, both weaning weights and annual growth were >= 30 kg higher, enabling 86-100% of HIM steers to exceed 500 kg at 2.5 years of age. Very few contemporary SLIM steers reached this target. HIM was most profitably applied to steers. Where HIM was able to achieve high pregnancy rates in yearlings, its application was recommended in females. Well managed, appropriate HIM systems increased profits by around $15/adult equivalent at prevailing beef and supplement prices. However, a 20% supplement price rise without a commensurate increase in values for young slaughter steers would generally eliminate this advantage. This study demonstrated the complexity of pro. table application of research outcomes to commercial business, even when component research suggests that specific strategies may increase growth and reproductive efficiency and/or be more pro. table. Because of the higher level of management required, higher costs and returns, and higher susceptibility to market changes and disease, HIM systems should only be applied after SLIM systems are well developed. To increase profitability, any strategy must ultimately either increase steer growth and sale values and/or enable a shift to high pregnancy rates in yearling heifers.

PI09004 New Generation Pineapple Breeding Project

To work with a major industry production/marketing unit to develop new pineapple varieties with good plant vigour, high yields and post-harvest attributes and eating quality equal to or better than the standard industry varieties 73-50 and MD2 under commercial production systems. The project uses previously developed germplasm as parental material.

Factors associated with calf mortality in tropically adapted beef breeds managed in extensive Australian production systems

Data from 9296 calves born to 2078 dams over 9 years across five sites were used to investigate factors associated with calf mortality for tropically adapted breeds (Brahman and Tropical Composite) recorded in extensive production systems, using multivariate logistic regression. The average calf mortality pre-weaning was 9.5% of calves born, varying from 1.5% to 41% across all sites and years. In total, 67% of calves that died did so within a week of their birth, with cause of death most frequently recorded as unknown. The major factors significantly (P < 0.05) associated with mortality for potentially large numbers of calves included the specific production environment represented by site-year, low calf birthweight (more so than high birthweight) and horn status at branding. Almost all calf deaths post-branding (assessed from n = 8348 calves) occurred in calves that were dehorned, totalling 2.1% of dehorned calves and 15.9% of all calf deaths recorded. Breed effects on calf mortality were primarily the result of breed differences in calf birthweight and, to a lesser extent, large teat size of cows; however, differences in other breed characteristics could be important. Twin births and calves assisted at birth had a very high risk of mortality, but <1% of calves were twins and few calves were assisted at birth. Conversely, it could not be established how many calves would have benefitted from assistance at birth. Cow age group and outcome from the previous season were also associated with current calf mortality; maiden or young cows (<4 years old) had increased calf losses overall. More mature cows with a previous outcome of calf loss were also more likely to have another calf loss in the subsequent year, and this should be considered for culling decisions. Closer attention to the management of younger cows is warranted to improve calf survival.

Screening and breeding for genetic resistance to anthracnose in mango

Postharvest diseases remain a significant constraint to the transport, storage and marketing of mangoes. The two main ones are anthracnose and stem end rot. Anthracnose caused by Colletotrichum gloeosporioides is the more wide-spread of the two. Varieties within Mangifera indica are known to vary in their level of reactions to anthracnose; however, the best tolerance in current commercial cultivars is not sufficient to eliminate the need for pre- and postharvest fungicides treatments. A screening program was initiated in mango accessions in the Australian National Mango Genebank to look for any significant resistance to C. gloeosporioides in fruit as they ripened. Screening was conducted by rating reactions to natural infection of anthracnose and reactions to artificially inoculating fruit with virulent isolates of C. gloeosporioides. A range of reactions to the pathogen were identified, with strong resistance found in one accession of the species M. laurina. This accession was used as the pollen parent in a controlled crossing program with a M. indica hybrid from the Australian Mango Breeding Program (AMBP). Sixty successful hybrids between the species have been generated. The hybrid population will be screened for resistance to anthracnose and used for gene discovery investigations to identify markers for anthracnose resistance.

Allelopathy for weed control in agricultural systems

Weeds are a hidden foe for crop plants, interfering with their functions and suppressing their growth and development. Yield losses of ∼34 are caused by weeds among the major crops, which are grown worldwide. These yield losses are higher than the losses caused by other pests in the crops. Sustainable weed management is needed in the wake of a huge decline in crop outputs due to weed pressure. A diversity in weed management tools ensures sustainable weed control and reduces chances of herbicide resistance development in weeds. Allelopathy as a tool, can be importantly used to combat the challenges of environmental pollution and herbicide resistance development. This review article provides a recent update regarding the practical application of allelopathy for weed control in agricultural systems. Several studies elaborate on the significance of allelopathy for weed management. Rye, sorghum, rice, sunflower, rape seed, and wheat have been documented as important allelopathic crops. These crops express their allelopathic potential by releasing allelochemicals which not only suppress weeds, but also promote underground microbial activities. Crop cultivars with allelopathic potentials can be grown to suppress weeds under field conditions. Further, several types of allelopathic plants can be intercropped with other crops to smother weeds. The use of allelopathic cover crops and mulches can reduce weed pressure in field crops. Rotating a routine crop with an allelopathic crop for one season is another method of allelopathic weed control. Importantly, plant breeding can be explored to improve the allelopathic potential of crop cultivars. In conclusion, allelopathy can be utilized for suppressing weeds in field crops. Allelopathy has a pertinent significance for ecological, sustainable, and integrated weed management systems.

High-throughput Phenotyping of Wheat Seminal Root Traits in a Breeding Context

Water availability is a major limiting factor for wheat (Triticum aestivum L.) in rain-fed agricultural systems worldwide. Root architecture has important functional implications for the timing and extent of soil water extraction, yet selection for root traits in wheat breeding programs has been largely limited due to the lack of suitable phenotyping methods. The aim of this research was to develop a low-cost high-throughput phenotyping method to facilitate selection for desirable root traits. We developed a method to assess ‘seminal root angle’ and ‘seminal root number’ in seedlings – two proxy traits associated to root architecture of mature wheat plants (1). The method involves measuring the angle between the first pair of seminal roots and the number of roots of wheat seedlings grown in transparent pots (Figure 1). Images captured at 5 to 10 days after sowing are analyzed to calculate seminal root angle and number. Performing this technique under “speed breeding” conditions (plants grown at a density of 600 plants / m2, under controlled temperature and constant light) allows the selection based on the desired root traits of up to 5 consecutive generations within 12 months. Alternatively, when focusing only on germplasm screening, up to 52 successive phenotypic assays can be conducted within 12 months. This approach has been shown to be highly reproducible, it requires little resource (time, space, and labour) and can be used to rapidly enrich breeding populations with desirable alleles for narrow root angle and a high number of seminal roots to indirectly target the selection of deeper root system with higher branching at depth. Such root characteristics are highly desirable in wheat to cope with the climate model projections, especially in summer rainfall dominant regions including some Australian, Indian, South American and African cropping regions, where winter crops mainly rely on deep stored water.

Integrating Rapid Phenotyping and Speed Breeding to Improve Stay-Green and Root Adaptation of Wheat in Changing, Water-Limited, Australian Environments

Temperatures have increased and in-crop rainfall decreased over recent decades in many parts of the Australian wheat cropping region. With these trends set to continue or intensify, improving crop adaptation in the face of climate change is particularly urgent in this, already drought-prone, cropping region. Importantly, improved performance under water-limitation must be achieved while retaining yield potential during more favourable seasons. A multi-trait-based approach to improve wheat yield and yield stability in the face of water-limitation and heat has been instigated in northern Australia using novel phenotyping techniques and a nested association mapping (NAM) approach. An innovative laboratory technique allows rapid root trait screening of hundreds of lines. Using soil grown seedlings, the method offers significant advantages over many other lab-based techniques. Another recently developed method allows novel stay-green traits to be quantified objectively for hundreds of genotypes in standard field trial plots. Field trials in multiple locations and seasons allow evaluation of targeted trait values and identification of superior germplasm. Traits, including yield and yield components are measured for hundreds of NAM lines in rain fed environments under various levels of water-limitation. To rapidly generate lines of interest, the University of Queensland “speed breeding” method is being employed, allowing up to 7 plant generations per annum. A NAM population of over 1000 wheat recombinant inbred lines has been progressed to the F5 generation within 18 months. Genotyping the NAM lines with the genome-wide DArTseq molecular marker system provides up to 40,000 markers. They are now being used for association mapping to validate QTL previously identified in bi-parental populations and to identify novel QTL for stay-green and root traits. We believe that combining the latest techniques in physiology, phenotyping, genetics and breeding will increase genetic progress toward improved adaptation to water-limited environments.

Improving cost-effectiveness of supplementation systems for breeder herds in northern Australia

Low level strategic supplements constitute one of the few options for northern beef producers to increase breeder productivity and profitability. Objectives of the project were to improve the cost-effectiveness of using such supplements and to improve supplement delivery systems. Urea-based supplements fed during the dry season can substantially reduce breeder liveweight loss and increase fertility during severe dry seasons. Also when fed during the late wet season these supplements increased breeder body liveweight and increased fertility of breeders in low body condition. Intake of dry lick supplements fed free choice is apparently determined primarily by the palatability of supplements relative to pasture, and training of cattle appears to be of limited importance. Siting of supplementation points has some effect on supplement intake, but little effect on grazing behaviour. Economic analysis of supplementation (urea, phosphorus or molasses) and weaning strategies was based on the relative efficacy of these strategies to maintain breeder body condition late in the dry season. Adequate body condition of breeders at this time of the year is needed to avoid mortality from under-nutrition and achieve satisfactory fertility of breeders during the following wet season. Supplements were highly cost-effective when they reduced mortality, but economic returns were generally low if the only benefit was increased fertility.